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- PDB-3f4b: Crystal structure of Plasmodium berghei Enoyl-acyl-carrier-protei... -

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Basic information

Entry
Database: PDB / ID: 3f4b
TitleCrystal structure of Plasmodium berghei Enoyl-acyl-carrier-protein reductase with TRICLOSAN
ComponentsEnoyl-acyl carrier protein reductase
KeywordsOXIDOREDUCTASE / PbENR / PbFabI / triclosan
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / nucleotide binding
Similarity search - Function
Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TRICLOSAN / Enoyl-acyl carrier protein reductase
Similarity search - Component
Biological speciesPlasmodium berghei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsSacchettini, J.C. / Tsai, H.-C.
CitationJournal: Cell Host Microbe / Year: 2008
Title: The fatty acid biosynthesis enzyme FabI plays a key role in the development of liver-stage malarial parasites.
Authors: Yu, M. / Kumar, T.R. / Nkrumah, L.J. / Coppi, A. / Retzlaff, S. / Li, C.D. / Kelly, B.J. / Moura, P.A. / Lakshmanan, V. / Freundlich, J.S. / Valderramos, J.C. / Vilcheze, C. / Siedner, M. / ...Authors: Yu, M. / Kumar, T.R. / Nkrumah, L.J. / Coppi, A. / Retzlaff, S. / Li, C.D. / Kelly, B.J. / Moura, P.A. / Lakshmanan, V. / Freundlich, J.S. / Valderramos, J.C. / Vilcheze, C. / Siedner, M. / Tsai, J.H. / Falkard, B. / Sidhu, A.B. / Purcell, L.A. / Gratraud, P. / Kremer, L. / Waters, A.P. / Schiehser, G. / Jacobus, D.P. / Janse, C.J. / Ager, A. / Jacobs, W.R. / Sacchettini, J.C. / Heussler, V. / Sinnis, P. / Fidock, D.A.
History
DepositionOct 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-acyl carrier protein reductase
B: Enoyl-acyl carrier protein reductase
C: Enoyl-acyl carrier protein reductase
D: Enoyl-acyl carrier protein reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,52912
Polymers143,7174
Non-polymers3,8128
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22880 Å2
ΔGint-214 kcal/mol
Surface area38330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.339, 121.200, 87.832
Angle α, β, γ (deg.)90.00, 108.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Enoyl-acyl carrier protein reductase /


Mass: 35929.336 Da / Num. of mol.: 4 / Fragment: UNP residues 75 to 396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium berghei (eukaryote) / Gene: pbfabI / Plasmid: pVP16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6TEI5, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-TCL / TRICLOSAN / Triclosan


Mass: 289.542 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H7Cl3O2 / Comment: antifungal, antibiotic, detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 100mM Tris pH 7.1, 14% PEG2000, 100mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.49→36.33 Å / Num. obs: 41328 / % possible obs: 94.98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 %

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NHG

1nhg


Resolution: 2.49→36.33 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2075 -RANDOM
Rwork0.1835 ---
obs0.1835 39254 92.2 %-
Refinement stepCycle: LAST / Resolution: 2.49→36.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8899 0 244 264 9407

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